1ay1: Difference between revisions

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-{{Seed}}
+<table cellpadding='5'><tr><td style='background-color: yellow;border:2px solid black;font-size:150%;'>
-{{Template:Possible_fraud}}
+WARNING: This structure was flagged as problematic. For additional information see '''2009, December:''' at [[Retractions and Fraud]].</td></tr></table>
-[[Image:1ay1.png|left|200px]]
+==ANTI TAQ FAB TP7==
+<StructureSection load='1ay1' size='340' side='right' caption='[[1ay1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ay1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AY1 FirstGlance]. <br>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ay1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ay1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ay1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ay1 PDBsum]</span></td></tr>
+</table>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ay/1ay1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+TP7, an antibody against Thermus aquaticus DNA polymerase I (TaqP), is used as a thermolabile switch in 'hot start' variations of PCR to minimize non-specific amplification events. Earlier studies have established that TP7 binds to the polymerase domain of TaqP, competes with primer template complex for binding and is a potent inhibitor of the polymerase activity of TaqP. We report crystallographic determination of the structure of an Fab fragment of TP7 and computational docking of the structure with the known three-dimensional structure of the enzyme. Our observations strongly suggest that the origin of inhibitory ability of TP7 is its binding to enzyme residues involved in DNA binding and polymerization mechanism. Although criteria unbiased by extant biochemical data have been used in identification of a putative solution, the resulting complex offers an eminently plausible structural explanation of biochemical observations. The results presented are of general significance for interpretation of docking experiments and in design of small molecular inhibitors of TaqP, that are not structurally similar to substrates, for use in PCR. Structural and functional similarities noted among DNA polymerases, and the fact that several DNA polymerases are pharmacological targets, make discovery of non-substrate based inhibitors of additional importance.
-<!--
+Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition.,Murali R, Helmer-Citterich M, Sharkey DJ, Scalice ER, Daiss JL, Sullivan MA, Krishna Murthy HM Protein Eng. 1998 Feb;11(2):79-86. PMID:9605541<ref>PMID:9605541</ref>
-The line below this paragraph, containing "STRUCTURE_1ay1", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1ay1|  PDB=1ay1  |  SCENE=  }}
-===ANTI TAQ FAB TP7===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+==See Also==
-<!--
+*[[Antibody|Antibody]]
-The line below this paragraph, {{ABSTRACT_PUBMED_9605541}}, adds the Publication Abstract to the page
+*[[Retractions and Fraud|Retractions and Fraud]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9605541 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9605541}}
+__TOC__
+</StructureSection>
-==About this Structure==
-AY1 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY1 OCA].
-==Reference==
-<ref group="xtra">PMID:9605541</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Daiss, J L.]]
+[[Category: Daiss, J L]]
-[[Category: Helmer-Citterich, M.]]
+[[Category: Helmer-Citterich, M]]
-[[Category: Murali, R.]]
+[[Category: Murali, R]]
-[[Category: Murthy, H M.K.]]
+[[Category: Murthy, H M.K]]
-[[Category: Scalice, E R.]]
+[[Category: Scalice, E R]]
-[[Category: Sharkey, D J.]]
+[[Category: Sharkey, D J]]
-[[Category: Sullivan, M A.]]
+[[Category: Sullivan, M A]]
 [[Category: Antibody]]
 [[Category: Enzyme inhibitor]]
@@ Line 39: / Line 47: @@
 [[Category: Immunoglobulin]]
 [[Category: Pcr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:51:00 2009''